Starting phenix.real_space_refine on Thu Jun 27 08:14:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pwl_17994/06_2024/8pwl_17994.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pwl_17994/06_2024/8pwl_17994.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pwl_17994/06_2024/8pwl_17994.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pwl_17994/06_2024/8pwl_17994.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pwl_17994/06_2024/8pwl_17994.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pwl_17994/06_2024/8pwl_17994.pdb" } resolution = 4.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.080 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 91 5.16 5 C 7769 2.51 5 N 2132 2.21 5 O 2274 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 12266 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 830, 6603 Classifications: {'peptide': 830} Link IDs: {'PTRANS': 38, 'TRANS': 791} Chain breaks: 2 Chain: "B" Number of atoms: 5663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5663 Classifications: {'peptide': 711} Link IDs: {'PTRANS': 29, 'TRANS': 681} Chain breaks: 2 Time building chain proxies: 7.08, per 1000 atoms: 0.58 Number of scatterers: 12266 At special positions: 0 Unit cell: (79.23, 136.776, 168.468, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 91 16.00 O 2274 8.00 N 2132 7.00 C 7769 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.62 Conformation dependent library (CDL) restraints added in 2.1 seconds 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2918 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 8 sheets defined 66.9% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 2 through 18 removed outlier: 4.311A pdb=" N GLU A 6 " --> pdb=" O GLU A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 32 Processing helix chain 'A' and resid 35 through 40 removed outlier: 3.853A pdb=" N ALA A 40 " --> pdb=" O PRO A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 52 Processing helix chain 'A' and resid 67 through 76 removed outlier: 3.704A pdb=" N ILE A 71 " --> pdb=" O SER A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 88 removed outlier: 3.674A pdb=" N GLY A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 108 Processing helix chain 'A' and resid 110 through 120 Processing helix chain 'A' and resid 133 through 142 removed outlier: 3.886A pdb=" N ASN A 141 " --> pdb=" O TRP A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 153 removed outlier: 3.592A pdb=" N ASP A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN A 152 " --> pdb=" O HIS A 148 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N HIS A 153 " --> pdb=" O ASP A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 175 removed outlier: 3.562A pdb=" N VAL A 170 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 186 Processing helix chain 'A' and resid 199 through 208 removed outlier: 3.919A pdb=" N PHE A 203 " --> pdb=" O THR A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 219 Processing helix chain 'A' and resid 231 through 238 Processing helix chain 'A' and resid 241 through 252 Processing helix chain 'A' and resid 253 through 260 removed outlier: 4.251A pdb=" N GLN A 257 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 260 " --> pdb=" O PHE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 282 removed outlier: 3.776A pdb=" N GLN A 275 " --> pdb=" O ASN A 271 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL A 276 " --> pdb=" O MET A 272 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 307 removed outlier: 3.664A pdb=" N GLU A 297 " --> pdb=" O THR A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 334 removed outlier: 3.572A pdb=" N LYS A 318 " --> pdb=" O ASP A 314 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY A 334 " --> pdb=" O VAL A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 383 removed outlier: 3.627A pdb=" N LYS A 358 " --> pdb=" O SER A 354 " (cutoff:3.500A) Proline residue: A 359 - end of helix removed outlier: 3.558A pdb=" N LEU A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A 363 " --> pdb=" O PRO A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 465 removed outlier: 3.563A pdb=" N MET A 461 " --> pdb=" O GLN A 457 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N CYS A 462 " --> pdb=" O ALA A 458 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N CYS A 463 " --> pdb=" O PHE A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 483 removed outlier: 3.607A pdb=" N PHE A 479 " --> pdb=" O ARG A 475 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N HIS A 483 " --> pdb=" O PHE A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 494 removed outlier: 3.733A pdb=" N PHE A 490 " --> pdb=" O VAL A 486 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 491 " --> pdb=" O LEU A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 501 removed outlier: 4.469A pdb=" N ASP A 500 " --> pdb=" O LYS A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 507 Processing helix chain 'A' and resid 508 through 515 removed outlier: 3.623A pdb=" N ARG A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 520 Processing helix chain 'A' and resid 525 through 537 removed outlier: 3.826A pdb=" N GLU A 529 " --> pdb=" O LYS A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 560 No H-bonds generated for 'chain 'A' and resid 558 through 560' Processing helix chain 'A' and resid 561 through 573 Processing helix chain 'A' and resid 574 through 581 Processing helix chain 'A' and resid 593 through 609 removed outlier: 3.788A pdb=" N VAL A 597 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 609 " --> pdb=" O SER A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 removed outlier: 3.578A pdb=" N VAL A 633 " --> pdb=" O ASN A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 654 Processing helix chain 'A' and resid 663 through 672 removed outlier: 3.653A pdb=" N TYR A 667 " --> pdb=" O THR A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 684 removed outlier: 3.613A pdb=" N VAL A 680 " --> pdb=" O ASN A 676 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE A 683 " --> pdb=" O ASP A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 695 Processing helix chain 'A' and resid 736 through 751 Processing helix chain 'A' and resid 753 through 766 Processing helix chain 'A' and resid 769 through 774 Processing helix chain 'A' and resid 777 through 787 Processing helix chain 'A' and resid 792 through 799 Processing helix chain 'A' and resid 810 through 823 removed outlier: 3.850A pdb=" N GLN A 814 " --> pdb=" O ASP A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 836 Processing helix chain 'A' and resid 887 through 901 Processing helix chain 'B' and resid 3 through 17 Processing helix chain 'B' and resid 26 through 39 Proline residue: B 36 - end of helix Processing helix chain 'B' and resid 42 through 52 Processing helix chain 'B' and resid 67 through 76 Processing helix chain 'B' and resid 78 through 87 removed outlier: 3.559A pdb=" N VAL B 82 " --> pdb=" O VAL B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 109 removed outlier: 3.621A pdb=" N LEU B 104 " --> pdb=" O THR B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 120 Processing helix chain 'B' and resid 133 through 142 removed outlier: 4.000A pdb=" N TRP B 137 " --> pdb=" O THR B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 152 Processing helix chain 'B' and resid 166 through 175 Processing helix chain 'B' and resid 176 through 186 removed outlier: 3.593A pdb=" N VAL B 180 " --> pdb=" O HIS B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 208 removed outlier: 3.613A pdb=" N PHE B 203 " --> pdb=" O THR B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 219 Processing helix chain 'B' and resid 231 through 240 removed outlier: 3.771A pdb=" N LEU B 235 " --> pdb=" O THR B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 252 Processing helix chain 'B' and resid 254 through 262 Processing helix chain 'B' and resid 269 through 280 removed outlier: 3.871A pdb=" N VAL B 276 " --> pdb=" O MET B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 309 removed outlier: 3.662A pdb=" N GLU B 297 " --> pdb=" O THR B 293 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL B 298 " --> pdb=" O SER B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 334 removed outlier: 3.627A pdb=" N PHE B 331 " --> pdb=" O PHE B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 383 Proline residue: B 359 - end of helix removed outlier: 4.130A pdb=" N TRP B 364 " --> pdb=" O LEU B 360 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU B 367 " --> pdb=" O LEU B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 465 removed outlier: 3.842A pdb=" N MET B 461 " --> pdb=" O GLN B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 483 removed outlier: 3.701A pdb=" N ILE B 477 " --> pdb=" O SER B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 494 removed outlier: 4.055A pdb=" N LEU B 487 " --> pdb=" O HIS B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 501 removed outlier: 3.983A pdb=" N ASP B 500 " --> pdb=" O LYS B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 507 removed outlier: 3.674A pdb=" N LEU B 506 " --> pdb=" O HIS B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 520 removed outlier: 3.664A pdb=" N SER B 513 " --> pdb=" O PRO B 509 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG B 514 " --> pdb=" O GLU B 510 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N HIS B 517 " --> pdb=" O SER B 513 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ILE B 518 " --> pdb=" O ARG B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 536 removed outlier: 3.523A pdb=" N HIS B 536 " --> pdb=" O TYR B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 573 Processing helix chain 'B' and resid 574 through 581 removed outlier: 3.602A pdb=" N LEU B 578 " --> pdb=" O ASN B 574 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN B 580 " --> pdb=" O ALA B 576 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY B 581 " --> pdb=" O LYS B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 610 removed outlier: 3.506A pdb=" N VAL B 597 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASN B 610 " --> pdb=" O ASN B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 614 Processing helix chain 'B' and resid 636 through 654 Processing helix chain 'B' and resid 663 through 672 Processing helix chain 'B' and resid 676 through 682 removed outlier: 3.732A pdb=" N VAL B 680 " --> pdb=" O ASN B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 696 removed outlier: 3.505A pdb=" N ALA B 688 " --> pdb=" O ASP B 684 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP B 696 " --> pdb=" O GLN B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 751 Processing helix chain 'B' and resid 753 through 766 removed outlier: 3.540A pdb=" N MET B 766 " --> pdb=" O GLN B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 774 Processing helix chain 'B' and resid 777 through 787 Processing sheet with id=AA1, first strand: chain 'A' and resid 555 through 557 removed outlier: 5.799A pdb=" N LEU A 555 " --> pdb=" O ARG A 585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 616 through 618 Processing sheet with id=AA3, first strand: chain 'A' and resid 709 through 714 Processing sheet with id=AA4, first strand: chain 'A' and resid 850 through 851 Processing sheet with id=AA5, first strand: chain 'A' and resid 859 through 863 removed outlier: 3.550A pdb=" N THR A 872 " --> pdb=" O LYS A 881 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 554 through 557 removed outlier: 6.063A pdb=" N LEU B 555 " --> pdb=" O ARG B 585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 616 through 618 Processing sheet with id=AA8, first strand: chain 'B' and resid 710 through 714 641 hydrogen bonds defined for protein. 1887 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.81 Time building geometry restraints manager: 5.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4104 1.34 - 1.46: 2639 1.46 - 1.58: 5644 1.58 - 1.69: 0 1.69 - 1.81: 140 Bond restraints: 12527 Sorted by residual: bond pdb=" CA THR A 351 " pdb=" C THR A 351 " ideal model delta sigma weight residual 1.524 1.534 -0.010 1.26e-02 6.30e+03 6.73e-01 bond pdb=" CB MET A 5 " pdb=" CG MET A 5 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 6.04e-01 bond pdb=" C MET A 35 " pdb=" N PRO A 36 " ideal model delta sigma weight residual 1.335 1.346 -0.010 1.36e-02 5.41e+03 5.94e-01 bond pdb=" C THR A 351 " pdb=" N PRO A 352 " ideal model delta sigma weight residual 1.335 1.344 -0.009 1.19e-02 7.06e+03 5.82e-01 bond pdb=" CB ASP A 500 " pdb=" CG ASP A 500 " ideal model delta sigma weight residual 1.516 1.535 -0.019 2.50e-02 1.60e+03 5.80e-01 ... (remaining 12522 not shown) Histogram of bond angle deviations from ideal: 98.26 - 105.41: 263 105.41 - 112.56: 6442 112.56 - 119.72: 4220 119.72 - 126.87: 5886 126.87 - 134.02: 164 Bond angle restraints: 16975 Sorted by residual: angle pdb=" CA MET A 1 " pdb=" CB MET A 1 " pdb=" CG MET A 1 " ideal model delta sigma weight residual 114.10 119.35 -5.25 2.00e+00 2.50e-01 6.89e+00 angle pdb=" C MET A 1 " pdb=" CA MET A 1 " pdb=" CB MET A 1 " ideal model delta sigma weight residual 110.10 115.03 -4.93 1.90e+00 2.77e-01 6.73e+00 angle pdb=" CB MET A 1 " pdb=" CG MET A 1 " pdb=" SD MET A 1 " ideal model delta sigma weight residual 112.70 120.24 -7.54 3.00e+00 1.11e-01 6.32e+00 angle pdb=" CB MET A 5 " pdb=" CG MET A 5 " pdb=" SD MET A 5 " ideal model delta sigma weight residual 112.70 120.11 -7.41 3.00e+00 1.11e-01 6.09e+00 angle pdb=" N THR A 351 " pdb=" CA THR A 351 " pdb=" C THR A 351 " ideal model delta sigma weight residual 109.81 115.15 -5.34 2.21e+00 2.05e-01 5.83e+00 ... (remaining 16970 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.25: 6772 16.25 - 32.50: 606 32.50 - 48.75: 155 48.75 - 65.01: 25 65.01 - 81.26: 10 Dihedral angle restraints: 7568 sinusoidal: 3069 harmonic: 4499 Sorted by residual: dihedral pdb=" CA TRP B 370 " pdb=" C TRP B 370 " pdb=" N LEU B 371 " pdb=" CA LEU B 371 " ideal model delta harmonic sigma weight residual 180.00 160.95 19.05 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA LYS A 358 " pdb=" C LYS A 358 " pdb=" N PRO A 359 " pdb=" CA PRO A 359 " ideal model delta harmonic sigma weight residual 180.00 161.53 18.47 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA MET A 749 " pdb=" C MET A 749 " pdb=" N THR A 750 " pdb=" CA THR A 750 " ideal model delta harmonic sigma weight residual -180.00 -162.24 -17.76 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 7565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1266 0.032 - 0.063: 487 0.063 - 0.095: 102 0.095 - 0.127: 48 0.127 - 0.158: 2 Chirality restraints: 1905 Sorted by residual: chirality pdb=" CG LEU A 371 " pdb=" CB LEU A 371 " pdb=" CD1 LEU A 371 " pdb=" CD2 LEU A 371 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.26e-01 chirality pdb=" CA THR A 351 " pdb=" N THR A 351 " pdb=" C THR A 351 " pdb=" CB THR A 351 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" CA ILE B 768 " pdb=" N ILE B 768 " pdb=" C ILE B 768 " pdb=" CB ILE B 768 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.87e-01 ... (remaining 1902 not shown) Planarity restraints: 2206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 358 " -0.034 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO A 359 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 359 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 359 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 100 " -0.029 5.00e-02 4.00e+02 4.35e-02 3.02e+00 pdb=" N PRO B 101 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 101 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 101 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 199 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO A 200 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 200 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 200 " -0.023 5.00e-02 4.00e+02 ... (remaining 2203 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2656 2.78 - 3.31: 12751 3.31 - 3.84: 20609 3.84 - 4.37: 24398 4.37 - 4.90: 38856 Nonbonded interactions: 99270 Sorted by model distance: nonbonded pdb=" OD1 ASP A 500 " pdb=" N HIS A 501 " model vdw 2.250 2.520 nonbonded pdb=" NH2 ARG B 527 " pdb=" O LEU B 775 " model vdw 2.328 2.520 nonbonded pdb=" O ALA B 18 " pdb=" NE ARG B 19 " model vdw 2.348 2.520 nonbonded pdb=" OG1 THR A 144 " pdb=" OG1 THR A 178 " model vdw 2.358 2.440 nonbonded pdb=" O GLU A 821 " pdb=" NH2 ARG A 828 " model vdw 2.362 2.520 ... (remaining 99265 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 335 or resid 353 through 787)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.840 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 34.350 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6642 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12527 Z= 0.114 Angle : 0.510 7.543 16975 Z= 0.243 Chirality : 0.037 0.158 1905 Planarity : 0.003 0.051 2206 Dihedral : 13.554 81.257 4650 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.21), residues: 1529 helix: -0.02 (0.17), residues: 951 sheet: 1.37 (0.60), residues: 81 loop : -0.14 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 364 HIS 0.006 0.001 HIS B 765 PHE 0.014 0.001 PHE B 476 TYR 0.016 0.001 TYR B 632 ARG 0.002 0.000 ARG A 451 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.8134 (ttt) cc_final: 0.7601 (ttt) REVERT: B 447 MET cc_start: 0.6652 (ppp) cc_final: 0.6400 (ppp) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1929 time to fit residues: 51.7974 Evaluate side-chains 137 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 10.0000 chunk 116 optimal weight: 0.0770 chunk 64 optimal weight: 0.0030 chunk 39 optimal weight: 0.6980 chunk 78 optimal weight: 30.0000 chunk 62 optimal weight: 20.0000 chunk 120 optimal weight: 0.8980 chunk 46 optimal weight: 9.9990 chunk 73 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 139 optimal weight: 10.0000 overall best weight: 0.4948 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 12527 Z= 0.147 Angle : 0.541 8.338 16975 Z= 0.279 Chirality : 0.038 0.147 1905 Planarity : 0.004 0.049 2206 Dihedral : 3.613 17.598 1659 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.21), residues: 1529 helix: 0.46 (0.17), residues: 969 sheet: 1.37 (0.61), residues: 81 loop : -0.06 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 364 HIS 0.008 0.001 HIS B 765 PHE 0.024 0.001 PHE B 764 TYR 0.011 0.001 TYR A 288 ARG 0.003 0.000 ARG B 322 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 MET cc_start: 0.7078 (ptp) cc_final: 0.6379 (ptp) REVERT: A 500 ASP cc_start: 0.8166 (p0) cc_final: 0.7787 (p0) REVERT: A 766 MET cc_start: 0.9338 (mtm) cc_final: 0.9130 (mtt) REVERT: B 39 MET cc_start: 0.8335 (mpp) cc_final: 0.7915 (mpp) REVERT: B 322 ARG cc_start: 0.3647 (ttt180) cc_final: 0.3222 (tpt170) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1978 time to fit residues: 51.5542 Evaluate side-chains 136 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 30.0000 chunk 43 optimal weight: 0.3980 chunk 116 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 140 optimal weight: 9.9990 chunk 151 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 47 optimal weight: 0.4980 chunk 112 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN B 70 HIS B 483 HIS ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12527 Z= 0.141 Angle : 0.525 7.878 16975 Z= 0.267 Chirality : 0.038 0.144 1905 Planarity : 0.004 0.048 2206 Dihedral : 3.678 20.227 1659 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.07 % Allowed : 3.87 % Favored : 96.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.22), residues: 1529 helix: 0.62 (0.17), residues: 968 sheet: 1.29 (0.61), residues: 81 loop : 0.13 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 370 HIS 0.009 0.001 HIS B 765 PHE 0.026 0.001 PHE B 764 TYR 0.012 0.001 TYR B 460 ARG 0.002 0.000 ARG A 325 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 169 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.8089 (ttt) cc_final: 0.7756 (ttt) REVERT: A 467 MET cc_start: 0.7214 (ptp) cc_final: 0.6771 (ptt) REVERT: A 500 ASP cc_start: 0.8443 (p0) cc_final: 0.7956 (p0) REVERT: A 740 TYR cc_start: 0.8957 (t80) cc_final: 0.8190 (t80) REVERT: A 766 MET cc_start: 0.9363 (mtm) cc_final: 0.9056 (mpp) outliers start: 1 outliers final: 0 residues processed: 170 average time/residue: 0.1986 time to fit residues: 52.5854 Evaluate side-chains 131 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 20.0000 chunk 105 optimal weight: 0.0970 chunk 72 optimal weight: 8.9990 chunk 15 optimal weight: 0.2980 chunk 66 optimal weight: 0.5980 chunk 94 optimal weight: 0.8980 chunk 140 optimal weight: 10.0000 chunk 148 optimal weight: 50.0000 chunk 73 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 HIS B 483 HIS ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 12527 Z= 0.134 Angle : 0.534 8.631 16975 Z= 0.264 Chirality : 0.038 0.150 1905 Planarity : 0.004 0.048 2206 Dihedral : 3.686 18.949 1659 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.22), residues: 1529 helix: 0.64 (0.17), residues: 963 sheet: 1.17 (0.61), residues: 81 loop : 0.06 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 137 HIS 0.017 0.001 HIS B 765 PHE 0.022 0.001 PHE A 490 TYR 0.015 0.001 TYR A 802 ARG 0.003 0.000 ARG A 475 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.8104 (ttt) cc_final: 0.7718 (ttt) REVERT: A 317 MET cc_start: 0.8134 (mtm) cc_final: 0.7874 (mtm) REVERT: A 467 MET cc_start: 0.7279 (ptp) cc_final: 0.6810 (ptt) REVERT: A 500 ASP cc_start: 0.8432 (p0) cc_final: 0.8000 (p0) REVERT: A 766 MET cc_start: 0.9340 (mtm) cc_final: 0.9037 (mpp) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.1994 time to fit residues: 52.9392 Evaluate side-chains 134 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.9897 > 50: distance: 13 - 31: 3.345 distance: 23 - 45: 24.692 distance: 31 - 32: 9.270 distance: 32 - 33: 19.241 distance: 32 - 35: 18.370 distance: 33 - 34: 29.131 distance: 33 - 37: 41.285 distance: 35 - 36: 11.773 distance: 37 - 38: 10.202 distance: 38 - 39: 21.285 distance: 38 - 41: 5.504 distance: 39 - 40: 17.398 distance: 41 - 42: 12.859 distance: 41 - 43: 7.200 distance: 42 - 44: 11.355 distance: 45 - 46: 3.509 distance: 46 - 47: 5.048 distance: 46 - 49: 4.585 distance: 47 - 53: 4.118 distance: 48 - 81: 16.423 distance: 49 - 50: 6.778 distance: 50 - 51: 15.077 distance: 50 - 52: 5.632 distance: 53 - 54: 4.662 distance: 54 - 55: 7.579 distance: 54 - 57: 3.492 distance: 55 - 56: 14.201 distance: 55 - 60: 16.775 distance: 56 - 86: 22.576 distance: 57 - 58: 5.717 distance: 58 - 59: 5.250 distance: 60 - 61: 12.597 distance: 61 - 64: 9.324 distance: 62 - 63: 6.340 distance: 62 - 69: 5.126 distance: 63 - 95: 15.280 distance: 64 - 65: 5.384 distance: 65 - 66: 7.293 distance: 66 - 67: 19.379 distance: 66 - 68: 13.830 distance: 69 - 70: 5.155 distance: 70 - 71: 3.160 distance: 70 - 73: 5.898 distance: 71 - 72: 11.121 distance: 71 - 81: 4.180 distance: 72 - 103: 3.675 distance: 73 - 74: 4.462 distance: 74 - 75: 3.923 distance: 74 - 76: 6.410 distance: 76 - 78: 6.312 distance: 78 - 79: 4.341 distance: 79 - 80: 6.671 distance: 81 - 82: 6.548 distance: 82 - 83: 6.873 distance: 82 - 85: 10.350 distance: 83 - 86: 3.273 distance: 84 - 111: 6.331 distance: 86 - 87: 7.263 distance: 87 - 90: 9.406 distance: 88 - 89: 6.167 distance: 88 - 95: 5.478 distance: 90 - 91: 11.843 distance: 91 - 92: 4.163 distance: 92 - 93: 13.925 distance: 93 - 94: 12.218 distance: 96 - 97: 4.806 distance: 97 - 98: 7.298 distance: 98 - 125: 15.447 distance: 99 - 100: 13.425 distance: 100 - 101: 4.107 distance: 100 - 102: 7.095 distance: 103 - 104: 4.716 distance: 104 - 105: 3.334 distance: 104 - 107: 6.889 distance: 105 - 106: 10.263 distance: 105 - 111: 3.556 distance: 106 - 131: 16.012 distance: 107 - 108: 10.736 distance: 108 - 109: 8.383